That'd have to be broken down into several categories for me. You have some guys who are at the top of the MMA food chain because of their grappling, and then you have guys who aren't the best MMA fighters but are excellent submission grapplers.
I'd say Royler Gracie is definitely way up there. I'll be honest with you, I'm basing what I know about Royler Gracie from Eddie Bravo's book. But wasn't Royler dominating his cometition in ADCC up until Eddie? That's really nothing to blink at. Royler may not be an MMA champ but he's a really good grappler.
B.J. Penn without a doubt. He's great at both straight grappling and MMA. Choking out Matt Hughes is a mark of excellence in grappling; that really goes without saying. Hughes really knows his stuff on the ground.
When I think of grapplers in MMA, though, two guys come to mind: Sakuraba and Nogueira. They fight totally differently but they both adapt grappling to MMA in an amazing way.
Say what you want about Sakuraba. He has one of the most incredible top games I have ever seen. I can honestly say that other than Saku, I have never seen someone catch a Chute Boxe low roundhouse and turn it into a low single leg takedown. I still have no idea how Saku does that. I can do it in sparring, but that's with pads, lighter contact, and I'm not fighting Vanderlei Silva. He defeated Gracies (I know they're not invincible, but at the time, that was a pretty big thing) with submissions, and he makes the top game exciting. He passes the guard, and he's scientific in setting up his submissions. Sakuraba is by far one of the best MMA grapplers.
Nogueira also comes to mind. He has the perfect strategy: outbox you, and when you take him down, destroy you with his guard. He uses his guard offensively, which I love, because that's what I've learned to do (obviously not nearly as good as him, but I'm working on it). Instead of just holding on and hoping to get a better position, he fights from his guard. He grabs your wrists and you don't know whether he's going for a kimura or a triangle. He climbs his guard up, and when you think you have a better position, his open guard is great, too.
Fedor is definitely great on the ground, but I don't know if I'd think of him as a grappler as opposed to just a rounded MMA fighter. His gameplan varies for each opponent, whereas Saku, Nog, and Penn, it's going to be on the ground. Plus, during his fight with Nog, Fedor employed more of a ground and pound game. That takes grappling skill, but when I'm talking about grappling here, I mean submissions, too.
I don't know if you guys have heard of Joe Lauzon or Danny Lauzon, but keep your eyes and ears open. The Lauzon brothers are like the Penn brothers over here in Massachusetts. Joe is 21, and Danny is just about to turn 18 I think (or maybe he already turned 18). Neither of them wrestled in high school, but Joe picked up grappling, and then Danny followed. They both got REALLY good in an incredibly short amount of time. Joe's only been fighting for 3 years and he just recently fought Ivan Menjivar. At that weight class, Menjivar is ranked in the world, not just in North America. He lost, but still, to fight Ivan Menjivar after only 3 years of MMA (plus 18 months before he started fighting), is really good. I think Joe's pretty well rounded, and I'm sure Danny's stand up is great, but they're involved a lot in grappling. I competed in the teens division with Danny Lauzon in NAGA, and unfortunately I lost before I got a chance to fight him (he would've schooled me anyways, but I still want to fight him). Danny swept the division pretty much with ease. He didn't even look like he was having trouble. Joe started running his own grappling league here in Massachusetts, where you're guaranteed a good number of matches, and it's running really well. Seriously, keep your eyes open, because you are going to see at least one of the Lauzon brothers in UFC or Pride, without a doubt.